Bones messes up my model?
I think your problem is that the weights are automatic.... They mess up the model!

I found a good tutorial about rigging and animating in Blender and at the 11 minute he starts to show how to weight paint correctly. 

Link of the video: https://www.youtube.com/watch?v=mhQY2_gVoVg

I hope that helps!

Bye!